--- melting-4.3c.orig/debian/melting-gui.menu
+++ melting-4.3c/debian/melting-gui.menu
@@ -0,0 +1,7 @@
+?package(melting-gui):\
+ needs="X11"\
+ section="Applications/Science/Biology"\
+ title="Melting"\
+ command="/usr/bin/tkmelting"\
+ hints="Primer design"\
+ longtitle="Computes the melting temperature for a nucleic acid duplex."
--- melting-4.3c.orig/debian/README.Debian
+++ melting-4.3c/debian/README.Debian
@@ -0,0 +1,17 @@
+Meting for Debian
+─────────────────
+
+Notes about how this package was tested:
+
+After building locally on the developper’s computer, the programs melting and
+tkmelting were briefly tested before uploading the package to the Debian
+archive.
+
+ - melting was ran with the following command line:
+ melting -SAAAAAAAAAAAAAAA -HA -k0.01 -P0.01
+
+ - The tkmelting interface was invoked from the Gnome menu, and the meltin
+ temperature of 0.01 M of the AAAAAAAAAAAAAAA oligonucleotide was calculated
+ for a 0.01 M salt concentration.
+
+ -- Charles Plessy <plessy@debian.org> Fri, 20 Nov 2009 10:00:28 +0900
--- melting-4.3c.orig/debian/melting-gui.manpages
+++ melting-4.3c/debian/melting-gui.manpages
@@ -0,0 +1 @@
+DOC/tkmelting.1
--- melting-4.3c.orig/debian/reference
+++ melting-4.3c/debian/reference
@@ -0,0 +1,12 @@
+@article{NicolasLe Novere12012001,
+author = {Le Novere, Nicolas},
+title = {{MELTING, computing the melting temperature of nucleic acid duplex}},
+journal = {Bioinformatics},
+volume = {17},
+number = {12},
+pages = {1226-1227},
+doi = {10.1093/bioinformatics/17.12.1226},
+year = {2001},
+URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/12/1226},
+eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/17/12/1226.pdf}
+}
--- melting-4.3c.orig/debian/melting.docs
+++ melting-4.3c/debian/melting.docs
@@ -0,0 +1,4 @@
+DOC/melting
+DOC/melting.html
+DOC/melting.pdf
+README
--- melting-4.3c.orig/debian/control
+++ melting-4.3c/debian/control
@@ -0,0 +1,34 @@
+Source: melting
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy@debian.org>,
+ Andreas Tille <tille@debian.org>
+Build-Depends: debhelper (>= 7), quilt
+Standards-Version: 3.8.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/melting/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/melting/trunk/
+Homepage: http://www.ebi.ac.uk/compneur-srv/melting/
+
+Package: melting
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: melting-gui
+Description: compute the melting temperature of nucleic acid duplex
+ This program computes, for a nucleic acid duplex, the enthalpy, the
+ entropy and the melting temperature of the helix-coil
+ transitions. Three types of hybridisation are possible: DNA/DNA,
+ DNA/RNA, and RNA/RNA. The program first computes the hybridisation
+ enthalpy and entropy from the elementary parameters of each Crick's
+ pair by the nearest-neighbor method. Then the melting temperature is
+ computed. The set of thermodynamic parameters can be easily changed,
+ for instance following an experimental breakthrough.
+
+Package: melting-gui
+Architecture: all
+Depends: perl-tk, melting, ${misc:Depends}
+Description: graphical interface to compute the melting temperature of nucleic acid duplex
+ This package provides a graphical user interface for the “melting”
+ program, which computes for a nucleic acid duplex the enthalpy, the entropy
+ and the melting temperature of the helix-coil transitions.
--- melting-4.3c.orig/debian/melting.manpages
+++ melting-4.3c/debian/melting.manpages
@@ -0,0 +1 @@
+DOC/melting.1
--- melting-4.3c.orig/debian/melting.examples
+++ melting-4.3c/debian/melting.examples
@@ -0,0 +1,3 @@
+BIN/multi.pl
+BIN/profil.pl
+TEST
\ No newline at end of file
--- melting-4.3c.orig/debian/melting.doc-base
+++ melting-4.3c/debian/melting.doc-base
@@ -0,0 +1,14 @@
+Document: melting
+Title: The melting Manual
+Author: Nicolas Le Novère
+Abstract: This manual describes what melting is and how it can be used to
+ compute, for a nucleic acid duplex, the enthalpy, the entropy and the
+ melting temperature of the helix-coil transitions.
+Section: Science/Biology
+
+Format: pdf
+Files: /usr/share/doc/melting/melting.pdf.gz
+
+Format: HTML
+Index: /usr/share/doc/melting/melting.html
+Files: /usr/share/doc/melting/melting/*
--- melting-4.3c.orig/debian/changelog
+++ melting-4.3c/debian/changelog
@@ -0,0 +1,99 @@
+melting (4.3c-1) unstable; urgency=low
+
+ * New upstream release:
+ calls melting from the PATH with its base name (Closes: #549881).
+ * debian/melting/install:
+ multi.pl and profil.pl available in /usr/share/melting.
+ * debian/copyright refreshed to latest experimentations on the format.
+ * Target generating tkmelting manpage removed from debian/rules.
+ * Added various informations about upstream in debian/upstream-metadata.yaml.
+ * Document how to test melting and tkmelting in debian/README.Debian.
+
+ -- Charles Plessy <plessy@debian.org> Fri, 20 Nov 2009 10:00:28 +0900
+
+melting (4.3b-1) unstable; urgency=low
+
+ Tkmelting did not work in my tests.
+
+ * New upstream release, with new options for Tris, potassium and magnesium
+ concentrations, as well as support for inosine bases.
+
+ [ Charles Plessy ]
+ * debian/control:
+ - Moved bibliographic reference from the long description to a BibTeX file
+ (debian/reference, installed in /usr/share/doc/melting/reference).
+ - Incremented Standards-Version to reflect conformance with Policy 3.8.1
+ (no changes needed).
+ - Improved the description of melting-gui (Closes: #528999).
+ - Dropped versionned build-dependency on quilt (satisfied even in
+ oldstable).
+ - Build-Depend on dephelper 7 (debian/compat set to 7).
+ * debian/rules
+ - NNDIR=/usr/share/melting/NNFILES passed as a make argument instead of
+ through a patch (debian/patches/makefile.patch deleted).
+ - clean target rewritten so that debian/patches/makefile-clean.patch could
+ be deleted.
+ - Use ‘dh’ in binary-arch and binary-indep targets.
+ * Deleted debian/patches/melting.c_silent.patch and
+ debian/patches/melting.1_escape.patch cosmetic deviations from Upstream.
+ * debian/copyright updated and converted to latest version of the
+ machine-readable format.
+ * debian/tkmelting.1* and debian/melting-gui.desktop were adopted upstream and
+ deleted from the debian directory.
+
+ [ David Paleino ]
+ * Removed myself from Uploaders
+
+ [ Andreas Tille ]
+ * debian/control:
+ - Standards-Version: 3.8.3 (Added README.Source)
+ - s/Debian-Med/Debian Med/
+ * debian/patches/20_fix_manpage.patch: Fix typo in manpage
+
+ -- Andreas Tille <tille@debian.org> Wed, 30 Sep 2009 14:31:20 +0200
+
+melting (4.2h-3) unstable; urgency=low
+
+ * Changed the doc-base section according to the new policy.
+ * Updated my email address.
+
+ -- Charles Plessy <plessy@debian.org> Sun, 06 Jul 2008 18:11:48 +0900
+
+melting (4.2h-2) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * Moved the Homepage: field out from the package's description.
+ * Debian menu transition: updated debian/melting.doc-base.
+
+ [ David Paleino ]
+ * debian/tkmeltin.1 added - statically built
+ * debian/control:
+ - B-D updated (see above)
+ - added myself to Uploaders
+ - moved XS-Vcs-* to Vcs-*
+ * debian/rules:
+ - manpage statically built
+ - minor changes
+ * Updated to Standards-Version 3.7.3 (no changes needed)
+
+ [ Andreas Tille ]
+ * Added myself to uploaders
+ * debian/melting-gui.manpages: Fixed path to man page
+ * debian/melting.doc-base: Removed extra whitespace
+
+ -- Andreas Tille <tille@debian.org> Tue, 18 Mar 2008 10:32:48 +0100
+
+melting (4.2h-1) unstable; urgency=low
+
+ * New upstream version: switch to UTF-8 encoding.
+ * Corrects a typo in package description (Closes: #422983).
+ * Debian Menu transition: Apps/Science becomes Applications/Science/Biology.
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org> Mon, 20 Aug 2007 23:45:32 +0900
+
+melting (4.2g-1) unstable; urgency=low
+
+ * Initial release (Closes: #418691)
+
+ -- Charles Plessy <charles-debian-nospam@plessy.org> Sun, 22 Apr 2007 11:49:38 +0900
+
--- melting-4.3c.orig/debian/rules
+++ melting-4.3c/debian/rules
@@ -0,0 +1,67 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Build rules for melting. you can use this file without restriction.
+
+# This has to be exported to make some magic below work.
+export DH_OPTIONS
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+include /usr/share/quilt/quilt.make
+
+configure: configure-stamp
+configure-stamp:
+ dh_testdir
+ cp makefile.unices Makefile
+ touch $@
+
+build: patch configure build-stamp
+build-stamp:
+ $(MAKE) NNDIR=/usr/share/melting/NNFILES
+ touch $@
+
+clean: unpatch
+ dh_testdir
+ dh_testroot
+ $(RM) melting.o decode.o calcul.o melting
+ dh_clean build-arch-stamp build-indep-stamp configure-stamp Makefile
+
+install: install-indep install-arch
+install-indep:
+ dh_testdir
+ dh_testroot
+ dh_prep -i
+ dh_installdirs -i
+ dh_install -i
+ install -D BIN/tkmelting.pl $(CURDIR)/debian/melting-gui/usr/bin/tkmelting
+ install -m 644 -D BIN/melting.hlp $(CURDIR)/debian/melting-gui/usr/share/melting/melting.hlp
+ install -m 644 -D melting-gui.desktop $(CURDIR)/debian/melting-gui/usr/share/applications/melting-gui.desktop
+
+install-arch:
+ dh_testdir
+ dh_testroot
+ dh_prep -s
+ dh_installdirs -s
+# install melting $(CURDIR)/debian/melting/usr/bin
+ dh_install -s
+
+binary: binary-arch binary-indep
+binary-indep: build install
+ dh binary-indep
+binary-arch: build install-arch
+ dh binary-arch
+
+# This is useful to download the orig.gz sources before running svn-buildpackage
+tarballs:
+ [ -d ../tarballs ] || mkdir ../tarballs
+ uscan --force-download
+ mv ../melt* ../tarballs
+
+binary: binary-arch binary-indep
+.PHONY: build clean binary-indep binary-arch binary install install-indep install-arch configure
--- melting-4.3c.orig/debian/copyright
+++ melting-4.3c/debian/copyright
@@ -0,0 +1,35 @@
+Format: Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
+
+Name: Melting
+Contact: Nicolas Le Novère <lenov@ebi.ac.uk>
+ Marine Dumousseau <marine@ebi.ac.uk>
+Source: http://qa.debian.org/watch/sf.php/melting/melting4_3c.tar.gz
+
+Copyright: 1997–2009, Nicolas Le Novère <lenov@ebi.ac.uk>
+ 1997–2009, Marine Dumousseau <marine@ebi.ac.uk>
+License: GPL-2+
+
+ Melting is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ Melting is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+On Debian systems, the complete text of the GNU General Public License version
+2 can be found in ‘/usr/share/common-licenses/GPL-2’.
+
+Files: debian/*
+Copyright: 2007–2009 Charles Plessy <plessy@debian.org>
+ 2008 Andreas Tille <tille@debian.org>
+ 2008 David Paleino <d.paleino@gmail.com>
+License:
+ You can use, redistribute, modify
+ the packaging work as if it were in the public domain.
--- melting-4.3c.orig/debian/upstream-metadata.yaml
+++ melting-4.3c/debian/upstream-metadata.yaml
@@ -0,0 +1,21 @@
+DOI: 10.1093/bioinformatics/17.12.1226
+PubMed: 11751232
+Reference_author: Le Novère, Nicolas
+Reference_title: MELTING, computing the melting temperature of nucleic acid duplex
+Reference_journal: Bioinformatics
+Reference_volume: 17
+Reference_number: 12
+Reference_pages: 1226-1227
+Reference_year: 2001
+Reference_URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/12/1226
+Reference_eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/17/12/1226.pdf
+Reference:
+ author: Le Novère, Nicolas
+ title: MELTING, computing the melting temperature of nucleic acid duplex
+ journal: Bioinformatics
+ volume: 17
+ number: 12
+ pages: 1226-1227
+ year: 2001
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/12/1226
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/17/12/1226.pdf
--- melting-4.3c.orig/debian/README.source
+++ melting-4.3c/debian/README.source
@@ -0,0 +1,4 @@
+This packages uses the quilt patch system. Please read
+/usr/share/doc/quilt/README.source for more information.
+
+ -- Andreas Tille <tille@debian.org> Wed, 30 Sep 2009 14:31:20 +0200
--- melting-4.3c.orig/debian/melting.install
+++ melting-4.3c/debian/melting.install
@@ -0,0 +1,4 @@
+melting usr/bin
+NNFILES usr/share/melting
+BIN/multi.pl usr/share/melting
+BIN/profil.pl usr/share/melting
--- melting-4.3c.orig/debian/watch
+++ melting-4.3c/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/melting/melting(.*?)_(.*?)\.tar\.gz
--- melting-4.3c.orig/debian/compat
+++ melting-4.3c/debian/compat
@@ -0,0 +1 @@
+7
--- melting-4.3c.orig/debian/melting.dirs
+++ melting-4.3c/debian/melting.dirs
@@ -0,0 +1,3 @@
+usr/bin
+usr/share/melting
+usr/share/doc/melting
--- melting-4.3c.orig/debian/patches/tkmelting.patch
+++ melting-4.3c/debian/patches/tkmelting.patch
@@ -0,0 +1,25 @@
+Author: Charles Plessy
+Description: Find perl in /usr/bin, and use a different hardcoded path to the help.
+Forwarded: not yet.
+License: same as Melting itself.
+
+Index: melting4_3/BIN/tkmelting.pl
+===================================================================
+--- melting4_3.orig/BIN/tkmelting.pl
++++ melting4_3/BIN/tkmelting.pl
+@@ -1,4 +1,5 @@
+-eval '(exit $?0)' && eval 'exec perl -S $0 ${1+ "$@"}' && eval 'exec perl -S $0 $argv:q' if 0;
++#!/usr/bin/perl
++#eval '(exit $?0)' && eval 'exec perl -S $0 ${1+ "$@"}' && eval 'exec perl -S $0 $argv:q' if 0;
+
+ ##############################################################################
+ # MELTING #
+@@ -449,7 +450,7 @@
+ )->pack(-expand => 1,
+ -fill => 'both'
+ );
+- open(FH,"melting.hlp") || die "unable to open melting.hlp";
++ open(FH,"/usr/share/melting/melting.hlp") || die "unable to open melting.hlp";
+ while (<FH>){
+ $helpText->insert('end', $_);
+ }
--- melting-4.3c.orig/debian/patches/20_fix_manpage.patch
+++ melting-4.3c/debian/patches/20_fix_manpage.patch
@@ -0,0 +1,13 @@
+Author: Andreas Tille <tille@debian.org>
+Description: Fix typo in manpage
+--- melting4_3b.orig/DOC/melting.1
++++ melting4_3b/DOC/melting.1
+@@ -55,7 +55,7 @@
+ (SantaLucia et al 1996),
+ .I sug96a.nn
+ (Sugimoto et al 1996)
+-.Isan04a.nn
++.I san04a.nn
+ (Santalucia et al 2004)
+ (DNA/DNA),
+ .I fre86a.nn
--- melting-4.3c.orig/debian/patches/series
+++ melting-4.3c/debian/patches/series
@@ -0,0 +1,2 @@
+tkmelting.patch
+20_fix_manpage.patch
![[patchlogo]](http://patch-tracker.debian.org/static/img/swirlpatch.png)